Additional file 1: of Early life diet conditions the molecular response to post-weaning protein restriction in the mouse

Table S1. Compositions of the control (CT) diet and the protein restricted (PR) diet. Table S2. List of all male mice studied with each litter represented by the first two numbers and letter of each ID. Table S3. Sequences of primers used for targeted analysis of DNA methylation at rDNA CpG −133 and the imprinted regions MEST, MCTS2, NESP and IGF2/H19. Figure S1. Growth rates of mice and lengths at death in each group. Figure S2. Absolute and relative organ weights. Figure S3. Absolute and relative adipose tissue deposit weights. Figure S4. Sperm small RNA size distribution analysis and sperm purity analysis. Figure S5. Read length distribution of reads mapping to the genome that also map to different classes of small RNA, normalised by total number of reads mapping to the genome. Figure S6. Maternal weight, food intake and litter size data. Figure S7. %A/C and CpG –133 meth % distribution in four diet groups. Figure S8. Growth trajectories plotted by pre-weaning litter size (including females). Figure S9. Pre-weaning litter size (including females) has no impact on CpG –133 A meth % in any of the groups. Supplementary methods. Rationale and explanation of the use of a linear model and robust standard errors to analyse the relationship between %A and CpG –133 A meth % instead of using litter averages or individuals from the same litter without correction for relatedness. R script used to perform the analysis is also included. (DOCX 1338 kb

Additional file 3: Table S2. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

Table containing the annotated information of the 1,807 experiment 2 only senDMPs. (CSV 539 kb

Additional file 6: Table S7. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

Panther DB pathway analysis of the 725 agree senDMPs. (XLSX 11 kb

Additional file 1: Figure S1. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

Model of senescence barriers in cultured HMECs. Figure S2. Morphology of DS cells following transfection. Figure S3. Comparison of the methylation state between EP and DS technical replicates for experiment 1. Figure S4. Comparison of the methylation state between EP and DS technical replicates for experiment 2. Figure S5. Comparison of average methylation between experiment 1 and 2 for EP and DS cells. Figure S6. Genomic feature analysis of senDMPs. Figure S7. The FACs sorting protocol. Figure S8. Decreased expression of p16 following reversal. Figure S9. Decreased expression of IL-6 and IL-8 following reversal. Figure S10. Increased expression of Polycomb proteins following reversal. Figure S11. Random permutation tests for hyper and hypo methylated Cpg sites. Figure S12. Average beta values for senDMPs in normal breast tissue samples. Figure S13. Average beta values for experiment 1 only senDMPs in eight different tissues. Figure S14. Average beta values for experiment 2 only senDMPs in eight different tissues. Figure S15. Average beta values for agree only senDMPs in eight different tissues. Figure S16. Plot showing the fraction of hypersenDMPs that showed a positive methylation and genotype correlation and hypo-senDMPs that showed a negative methylation genotype correlation (red) for different correlation cut offs. (DOC 2.43 mb

Большевик. 1940. № 020

Table containing the annotated information of the senescence associated probes reaching 0.01 FDR and beta value difference >0.3 in both experiment 1 and experiment 2 which are located on chrX. (CSV 1 kb

beta_normalised_bmiq

Contains normalised beta values for each CpG which passed QC from 450K array. Each column is a sample and each row is CpG. The first column contains CpG identifiers

Additional file 1: of Correlation of an epigenetic mitotic clock with cancer risk

Blood reference DNA methylation data matrix in Excel format. Detailed legend in file. (XLS 85 kb

Additional file 2: of Correlation of an epigenetic mitotic clock with cancer risk

The 385 PCGT CpGs that make up epiTOC. Detailed legend in file. (XLS 205 kb

Additional file 3: of Correlation of an epigenetic mitotic clock with cancer risk

Supplementary information document with all supplementary figures and their legends. (PDF 1902 kb

Additional file 5: of Correlation of an epigenetic mitotic clock with cancer risk

epiTOCcpgs.RData. An R object data file containing the 450 k probe IDs of the 385 PCGT CpGs that make up epiTOC. (RDATA 1 kb